---
title: "CE4 - Dashboard COVID-19"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    source_code: embed
    social: menu
    theme: cosmo
    self_contained: FALSE 
    fig_mobile: TRUE
---



```{r libraries, message=F, warning=F}
library(flexdashboard)
library(rio)
library(tidyverse)
library(XML)
library(httr)
library(RCurl)
library(sf)
library(lubridate)
library(leaflet)
library(colorspace)
library(DT)
library(zoo)
library(slider)
library(plotly)
library(waffle)
library(extrafont)
library(plyr)
library(extrafont)
library(waffle)
library(RColorBrewer)
library(fontawesome)
options(scipen=999)
```

```{r imports, message=F, warning=F, include = F, echo =F}
nac <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true")

dep <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true", sheet = 2)

pop <- read_csv("data/peru_pop_stratum.csv") %>%
  group_by(dep_adm1) %>%
  dplyr::summarise(pop = sum(N)) %>%
  dplyr::mutate(REGION = toupper(dep_adm1))


Paises_LATAM <- c("Argentina","Bolivia","Brazil","Chile","Colombia","Ecuador","Mexico","Peru","Uruguay","Venezuela")
LATAM <- read_csv ("https://covid.ourworldindata.org/data/owid-covid-data.csv") 

shp <- st_read("Limite_departamental", stringsAsFactors = F)%>% 
  st_transform(4326) %>% 
  dplyr::select(Departamento = NOMBDEP)
```

```{r global, message=F, warning=F}
c.date <- max(dep$Fecha)
y.date <- as.Date(c.date) - 1 
today <- ymd(Sys.Date())
f.date <- min(dep$Fecha)

# https://stackoverflow.com/questions/6461209/how-to-round-up-to-the-nearest-10-or-100-or-x
# Rounds Up to a nice number, defined as a number divisible by those in the vector.
# Some other good choices of the "nice" vector above are: 1:10, c(1,5,10), seq(1, 10, 0.1),c(1,2,4,5,6,8,10)

roundUpNice <- function(x, nice=c(1,2,5,6,10)) {
  if(length(x) != 1) stop("'x' must be of length 1")
  10^floor(log10(x)) * nice[[which(x <= 10^floor(log10(x)) * nice)[[1]]]]
}
# roundUpNice(max(nac$pos.new))/5

```

```{r plotly, message=F, warning=F}
icon_svg_path <- "M256 8C119.043 8 8 119.083 8 256c0 136.997 111.043 248 248 248s248-111.003 248-248C504 119.083 392.957 8 256 8zm0 110c23.196 0 42 18.804 42 42s-18.804 42-42 42-42-18.804-42-42 18.804-42 42-42zm56 254c0 6.627-5.373 12-12 12h-88c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h12v-64h-12c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h64c6.627 0 12 5.373 12 12v100h12c6.627 0 12 5.373 12 12v24z"
# icon_svg_path = "M19.404,6.65l-5.998-5.996c-0.292-0.292-0.765-0.292-1.056,0l-2.22,2.22l-8.311,8.313l-0.003,0.001v0.003l-0.161,0.161c-0.114,0.112-0.187,0.258-0.21,0.417l-1.059,7.051c-0.035,0.233,0.044,0.47,0.21,0.639c0.143,0.14,0.333,0.219,0.528,0.219c0.038,0,0.073-0.003,0.111-0.009l7.054-1.055c0.158-0.025,0.306-0.098,0.417-0.211l8.478-8.476l2.22-2.22C19.695,7.414,19.695,6.941,19.404,6.65z M8.341,16.656l-0.989-0.99l7.258-7.258l0.989,0.99L8.341,16.656z M2.332,15.919l0.411-2.748l4.143,4.143l-2.748,0.41L2.332,15.919z M13.554,7.351L6.296,14.61l-0.849-0.848l7.259-7.258l0.423,0.424L13.554,7.351zM10.658,4.457l0.992,0.99l-7.259,7.258L3.4,11.715L10.658,4.457z M16.656,8.342l-1.517-1.517V6.823h-0.003l-0.951-0.951l-2.471-2.471l1.164-1.164l4.942,4.94L16.656,8.342z"


icon_svg_path <-"M12.871,9.337H7.377c-0.304,0-0.549,0.246-0.549,0.549c0,0.303,0.246,0.55,0.549,0.55h5.494c0.305,0,0.551-0.247,0.551-0.55C13.422,9.583,13.176,9.337,12.871,9.337z M15.07,6.04H5.179c-0.304,0-0.549,0.246-0.549,0.55c0,0.303,0.246,0.549,0.549,0.549h9.891c0.303,0,0.549-0.247,0.549-0.549C15.619,6.286,15.373,6.04,15.07,6.04z M17.268,1.645H2.981c-0.911,0-1.648,0.738-1.648,1.648v10.988c0,0.912,0.738,1.648,1.648,1.648h4.938l2.205,2.205l2.206-2.205h4.938c0.91,0,1.648-0.736,1.648-1.648V3.293C18.916,2.382,18.178,1.645,17.268,1.645z M17.816,13.732c0,0.607-0.492,1.1-1.098,1.1h-4.939l-1.655,1.654l-1.656-1.654H3.531c-0.607,0-1.099-0.492-1.099-1.1v-9.89c0-0.607,0.492-1.099,1.099-1.099h13.188c0.605,0,1.098,0.492,1.098,1.099V13.732z"

infobutton <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos acumulados en escala logarítmica desde el día del primer reporte a nivel nacional. Las líneas punteadas corresponden a las pendientes de duplicación de casos cada 1 a 4 días; una pendiente más inclinada implica la duplicación de casos en menor tiempo.');
    }"
  )
)

plotly_config <- function(x) {
  x %>% config(locale = "es",
               displaylogo=F,
               modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                          "drawclosedpath","drawopenpath",
                                          "hoverClosestCartesian","hoverCompareCartesian",
                                          "toggleHover","toggleSpikelines"),
               modeBarButtonsToAdd = list(infobutton),
               responsive = T
  )
}


plotly_layout <- function(x) {
  x %>% layout(paper_bgcolor="black",
               plot_bgcolor="black",
               hoverdistance = 50,
               hovermode = "closest",
               dragmode="pan",
               margin = list(l=65, r=65, b=40, t=50),
               autosize=T
  )
}

# %>%
#   add_segments(x = "2020-03-15", xend = "2020-03-15", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="Estado de Emergencia",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#   ) %>%
#   add_segments(x = "2020-03-26", xend = "2020-03-26", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="1ra ampliación",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#                ) %>%
#   add_segments(x = "2020-04-23", xend = "2020-04-23", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="3ra ampliación",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#                ) 

```

```{r maps, message=F, warning=F}
map_tiles <- function(x) {
  x %>% 
    addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
             options = providerTileOptions(minZoom = 5, maxZoom = 6))
}

map_bounds <- function(x) {
  x %>% setMaxBounds(lng1 = -90.648918,
                     lat1 = 4.991423,
                     lng2 = -59.605965,
                     lat2 = -23.920121) 
}

map_poly <-  function(x,y,z) {
  x %>%
    addPolygons(fillColor = pal.cases(log(y)),
                weight = 2,
                opacity = 1,
                color = "white",
                dashArray = "",
                fillOpacity = 0.7,
                highlight = highlightOptions(
                  weight = 5,
                  color = "#666",
                  dashArray = "",
                  fillOpacity = 0.7,
                  bringToFront = TRUE),
                label = z,
                labelOptions = labelOptions(
                  style = list("font-weight" = "normal", padding = "3px 8px"),
                  textsize = "15px",
                  direction = "auto")) 
  
}

```

```{r deps, message=F, warning=F}
#### Procesamiento de los datos por región. ####

dep <- 
  dep %>% 
  dplyr::select(dat = Fecha,
                dep = REGION, 
                pos = Positivos_totales, 
                pos.imp = PositivosImputados_totales,
                pas =Fallecidos, 
                smp =Total_muestras
  ) %>% 
  dplyr::mutate(pas = pas %>% if_else(is.na(.), 0, .),
                dat = as.Date(dat)
  ) %>% 
  group_by(dep
  ) %>% 
  dplyr::mutate(pos.new = pos - lag(pos, n = 1),
                pos.imp.new = pos.imp - lag(pos.imp, n = 1),
                pas.new = lag(pas, n = 1),
                smp.new = lag(smp, n = 1),
                ratio.new = signif(pos.new/smp.new), digits = 3,
                days.start =as.numeric(dat-first(dat), unit="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                days.end = difftime(today, dat , units = c("days")),
                mav.pos.new = slide_dbl(pos.new, ~mean(.x, na.rm = TRUE), .before = 6),
  ) %>%
  merge(pop %>% 
          select(dep = REGION, pop)
  ) %>% 
  dplyr::mutate(pos.hab = pos/pop*100000,
                smp.hab = smp/pop*100000,
                pos.new.hab = smp/pop*100000,
                mav.pos.new.hab = mav.pos.new/pop*1000000)

dup.dep <- data.frame(dat = as.Date(seq(1,30, 1)+as.Date(c.date))) %>%
  dplyr::mutate(days.start = as.numeric(difftime(dat,f.date), units="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                dep= "LIMA",
                days.end = difftime(today, dat , units = c("days"))
  ) %>%
  bind_rows(dep)
#### Poligonos y data regional - Mapas #### 

geom.dep <- dep %>% 
  merge(shp, by.y = 'Departamento', by.x = 'dep', all.x = T) %>%
  st_as_sf(sf_column_name = 'geometry') 

rm(shp) # No more use for shp

#### Datos a nivel Nacional #### 

nac <- dep %>%
  select(-c("dep")) %>%
  group_by(dat) %>%
  dplyr::mutate_at(vars(-c("dat","dup.1","dup.2","dup.3","dup.4")),sum, na.rm = T) %>%
  dplyr::summarize_all(list(max)) %>%
  dplyr::mutate(days.end = difftime(today, dat , units = c("days")),
                days.start = as.numeric(difftime(dat,f.date), units="days"))

dup.nac <- data.frame(dat = as.Date(seq(1,30, 1)+today)) %>%
  dplyr::mutate(days.start = as.numeric(difftime(dat,f.date), units="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start)
  ) %>%
  bind_rows(nac)

#### Datos del día de hoy #### 
c.dep <- geom.dep %>%
  dplyr::filter(dat == c.date)

####  Formato Regiones Wide #### 
dep.pos <-  dep %>%
  select(dat,dep,pos,days.end) %>%
  spread(dep, pos) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

dep.pos2 <-  dep %>%
  select(dat,dep,pos,days.end,days.start) %>%
  spread(dep, pos) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

dep.mav.pos.new<-  dep %>%
  dplyr::select(dat,dep,days.end,mav.pos.new) %>%
  spread(dep, mav.pos.new) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 


dep.pos.imp.new <- dep %>%
  select(dat,dep,days.end,pos.imp.new) %>%
  spread(dep, pos.imp.new) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 
######################################
y<- dep.pos.imp.new 
colnames(y) <- paste(colnames(y), "2", sep = "_")

dep.pos_dep.pos.imp.new<- y %>% 
  select(-c("dat_2","days.end_2")) %>% 
  cbind(dep.pos)
######################################

### Wide dup 1 inicial
dep.pos2[nrow(dep.pos2)+30,] <- NA
dup.dep.1 <- dup.dep %>%
  select(dat,dep,days.end,days.start,dup.1) %>%
  spread(dep, dup.1) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

y<- dup.dep.1
colnames(y) <- paste(colnames(y), "2", sep = "_")

dup.dep.wide <- y %>% 
  select(-c("dat_2","days.end_2","days.start_2")) %>% 
  cbind(dep.pos2)

rm(dep.pos2)
### Wide dup 2
dup.dep.2 <- dup.dep %>%
  select(dat,dep,days.end,days.start,dup.2) %>%
  spread(dep, dup.2) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

y<- dup.dep.2
colnames(y) <- paste(colnames(y), "3", sep = "_")

dup.dep.wide <- y %>% 
  select(-c("dat_3","days.end_3","days.start_3")) %>% 
  cbind(dup.dep.wide)

### Wide dup 3
dup.dep.3 <- dup.dep %>%
  select(dat,dep,days.end,days.start,dup.3) %>%
  spread(dep, dup.3) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

y<- dup.dep.3
colnames(y) <- paste(colnames(y), "4", sep = "_")

dup.dep.wide <- y %>% 
  select(-c("dat_4","days.end_4","days.start_4")) %>% 
  cbind(dup.dep.wide)
### Wide dup 4
dup.dep.4 <- dup.dep %>%
  select(dat,dep,days.end,days.start,dup.4) %>%
  spread(dep, dup.4) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

y<- dup.dep.4
colnames(y) <- paste(colnames(y), "5", sep = "_")

dup.dep.wide <- y %>% 
  select(-c("dat_5","days.end_5","days.start_5")) %>% 
  cbind(dup.dep.wide)

#### LATAM #### 
LATAM <- LATAM %>%
  dplyr::filter(location %in% Paises_LATAM) %>%
  dplyr::mutate()%>% 
  group_by(location)%>% 
  dplyr::mutate(mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6),
                days.end = difftime(today, date , units = c("days")),
                days.start = as.numeric(difftime(date,f.date), units="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                mav.pos.new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6),
  )


dup.LATAM <- data.frame(date = as.Date(seq(1,30, 1)+as.Date(c.date))) %>%
  dplyr::mutate(days.start = as.numeric(difftime(date,f.date), units="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                location= "Peru"
  ) %>%
  bind_rows(LATAM)



```

```{r, message=F, warning=F}
vars.pmav.new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new.hab) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new.hab)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                             ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                    ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep

vars.mav.new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                             ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                    ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep
last.mav.new <- vars.mav.new[length(vars.mav.new)]


vars.pos <- dep %>%
  dplyr::select(dat,dep,pos) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(pos)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                             ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                    ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep
last.pos <- vars.pos[length(vars.pos)]

```

Casos Acumulados {.bg}
=====================================  

Mapas {.tabset data-width=200} 
-------------------------------------

### Casos

```{r, message=F, warning=F}
palette_1 <- c("#ffffff",
               "#fff3e3",
               "#ffe8c8",
               "#ffddac",
               "#ffd291",
               "#ffc775",
               "#ffbc59",
               "#ffb139", #ffa600
               "#ec9832",
               "#d8802c",
               "#c26926",
               "#ac5320",
               "#953e1b",
               "#7d2914",
               "#65150d",
               "#4e0000")

labels.total <-  sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette=palette_1, domain = log(c.dep$pos), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles() %>%
  map_poly (c.dep$pos,labels.total)  %>%
  addLegend("bottomleft", pal = pal.cases, values = log(c.dep$pos), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x)))) %>% 
  map_bounds ()

```

### Casos / 100k hab

```{r, message=F, warning=F}
labels.pos.hab <- sprintf(
  "%s
Casos/100k hab: %s",
  c.dep$dep, round(c.dep$pos.hab)) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette=palette_1, domain = log(c.dep$pos.hab), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles () %>%
  map_poly (c.dep$pos.hab,labels.pos.hab) %>%
  addLegend("bottomleft", pal = pal.cases, values = log(c.dep$pos.hab), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x)))) %>% map_bounds
```

Nacional {.tabset data-width=300} 
-------------------------------------

### Lineal

```{r, message=F, warning=F}
CA_2_1<- nac %>%
  plot_ly() %>%
  add_trace(x = ~dat, y = ~pos.new, 
            type = 'bar', name = 'Casos Nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'),
            yaxis="y") %>% 
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600',
                          maxdisplayed = 0),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}'),
            yaxis="y2") %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=roundUpNice(max(nac$pos.new)),
               text="2020-04-08",name="Pruebas Rápidas",
               hovertemplate = paste('%{text}'),
               width=2, 
               line = list(color = "#008f6a", 
                           width = 3, 
                           dash = "dot"))%>% 
  layout(title = '',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de Reporte",
                      color = "white",
                      tickformat= "%d-%b",
                      range = c(as.Date("2020-03-06"),
                                as.Date(c.date))),
         yaxis = list(side = 'left', title = 'Casos Nuevos por día', 
                      showgrid = T, gridcolor = "#818181", zeroline = F,
                      color = "#98cbe1",
                      range=list(0, roundUpNice(max(nac$pos.new))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac$pos.new))/5),
         yaxis2 = list(side = 'right', overlaying = "y3",
                       title = 'Casos acumulados (lineal)', 
                       showgrid = F, zeroline = F,
                       color = "#ffd29f",
                       range=list(0, roundUpNice(max(nac$pos))),
                       autotick=F,
                       tick0=0,
                       dtick=roundUpNice(max(nac$pos))/5),
         annotations = list(text = "Casos nuevos y acumulados - Perú",
                            x = 0.5, y = 1.1,
                            yref = "paper",xref = "paper",
                            xanchor = "middle",yanchor = "middle",
                            showarrow = FALSE,
                            font = list(size = 20,
                                        color = "white")),
         legend = list(orientation = "h",  
                       xanchor = "bottom",
                       yanchor = "middle",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white"))
  ) %>% 
  plotly_config() %>% 
  plotly_layout() %>%
  partial_bundle() 


```

### Duplicación

```{r, message=F, warning=F}

CA_2_2<-plot_ly(dup.nac)%>% 
  add_trace(x = ~dat, y = ~dup.1, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text") %>% 
  add_trace(x = ~dat, y = ~dup.2, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text") %>% 
  add_trace(x = ~dat, y = ~dup.3, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text") %>% 
  add_trace(x = ~dat, y = ~dup.4, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en cuatro (4) días",
            hoverinfo = "text")%>%
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"))   %>% 
  layout(title = list(text= '',
                      font = list(
                        size = 20,
                        color="white")),
         xaxis = list(title = list(text="Días desde el primer reporte",
                                   standoff = 15),
                      range = c(as.Date(min(f.date)),max(today+15)),
                      color ="white",
                      tickformat= "%d-%b", 
                      showgrid = F, zeroline = F),
         yaxis = list(side = 'left', 
                      title = list(text= 'Total de casos acumulados', 
                                   font = list(size = 16,
                                               color = "White"),
                                   standoff = 15),   
                      type="log", automargin = T,
                      range = c(min(0),max(6)), 
                      showgrid = T, gridcolor = "#818181", zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="ffd29f"),
         # legend = list(title=list(text="Casos acumulados se duplican en...",
         #                          font = list(color="white"),
         #                          side="top"),
         #               orientation = "h",
         #               yref = "paper",
         #               xref = "paper",
         #               xanchor = "right",
         #               yanchor = "bottom",  
         #               x = 1,
         #               y = 0.1,
         #               font = list(color = "white",
         #                           size = 10),
         #               bgcolor= 'rgba(0,0,0,0.7)', 
         #               automargin = T),
         annotations = list(yref = "paper",xref = "paper",
                            xanchor = "middle",yanchor = "middle",
                            showarrow = FALSE,
                            font = list(size = 20,
                                        color = "white"),
                            x=0.5,
                            y=1.1,
                            text='Casos acumulados - Perú',
                            showarrow=FALSE,
                            font = list(size = 20,
                                        color = "white"))
  ) %>%
  plotly_config( ) %>% 
  plotly_layout () %>%
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')%>%
    config(displayModeBar = TRUE)

CA_2_2
#fa("info-circle")


```

### LATAM - Lineal

```{r}
CA_1_1 <- LATAM %>%
  dplyr::filter(date>=as.Date("2020-03-06")) %>%
  highlight_key(~location) %>%
  plot_ly()%>%
  add_lines( x = ~date, text = ~location, colors = "YlOrRd",
             split=~location, y = ~total_cases,
             mode="lines",
             yaxis="y2",
             showlegend=F,
             line = list(width=0.75)
  ) %>%
  filter(location=="Peru") %>%
  add_trace( x = ~date, y = ~total_cases, 
             type = 'scatter',
             mode = 'lines', 
             name = 'Casos Acumulados',
             line = list(color = '#ffa600',
                         width=5),
             hovertemplate = ~paste('Fecha: %{x}',
                                    "
Casos Acumulados: %{y:.0f}
"),
             yaxis="y2",
             showlegend=F) %>%
  highlight(on = "plotly_hover", off = "plotly_doubleclick") %>%
  layout(title = list(text= '',
                      font = list(
                        size = 20,
                        color="white")),
         xaxis = list(range = c(as.Date("2020-03-06"),
                                c.date),
                      color = "white",
                      title ="Fecha de Reporte",
                      tickformat= "%d-%b"),
         yaxis2 = list(side = 'right',
                       title = '', 
                       showgrid = T, gridcolor = "#818181", zeroline = F,
                       color = "#ffd29f",
                       range=list(0, roundUpNice(max(LATAM$total_cases))),
                       autotick=F,
                       tick0=0,
                       dtick=roundUpNice(max(LATAM$total_cases))/5),
         annotations = list(text = "Casos acumulados - América Latina",
                            x = 0.5, y = 1.05,
                            yref = "paper",xref = "paper",
                            xanchor = "middle",yanchor = "middle",
                            showarrow = FALSE,
                            font = list(size = 20,
                                        color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         # legend = list(orientation = "h",  
         #               xanchor = "center",
         #               yanchor = "bottom",
         #               x = 0.5,
         #               y = -0.125,
         #               font = list(color = "white")),
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=65),
         showlegend=F) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )%>%
  partial_bundle() 
```

### LATAM - Logarítmica 

```{r}
CA_1_2 <- dup.LATAM %>%
  dplyr::filter(date>=as.Date("2020-03-06")) %>% plot_ly() %>%
  add_lines( x = ~date, text = ~location, colors = "YlOrRd",
             split=~location, y = ~total_cases,
             mode="lines",
             yaxis="y",
             showlegend=F,
             line = list(width=0.75)
  ) %>%
  filter(location=="Peru") %>%
  add_trace( x = ~date, y = ~total_cases, 
             type = 'scatter',
             mode = 'lines', 
             name = 'Casos Acumulados',
             line = list(color = '#ffa600',
                         width=5),
             hovertemplate = ~paste('Fecha: %{x}',
                                    "
Casos Acumulados: %{y:.0f}
"),
             yaxis="y",
             showlegend=F) %>%
  add_trace(x = ~date, y = ~dup.1, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            showlegend=F) %>% 
  add_trace(x = ~date, y = ~dup.2, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            showlegend=F) %>% 
  add_trace(x = ~date, y = ~dup.3, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            showlegend=F) %>% 
  add_trace(x = ~date, y = ~dup.4, 
            type = 'scatter',
            mode = 'lines', 
            name = 'Cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en cuatro (4) días",
            hoverinfo = "text",
            showlegend=F) %>%
  layout(title = list(text= '',
                      font = list(
                        size = 20,
                        color="white")),
         xaxis = list(range = c(as.Date("2020-03-06"),
                                max(dup.LATAM$date,na.rm=T)),
                      color = "white",
                      title ="Fecha de Reporte",
                      tickformat= "%d-%b",
                      showgrid=F),
         yaxis = list(side = 'left', 
                      title = list(text= 'Total de casos acumulados', 
                                   font = list(size = 16,
                                               color = "ffd29f"),
                                   standoff = 15),   
                      type="log", automargin = T,
                      range = c(min(0),max(6)), 
                      showgrid = F, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="White"),
         annotations = list(text = "Casos acumulados - América Latina",
                            x = 0.5, y = 1.05,
                            yref = "paper",xref = "paper",
                            xanchor = "middle",yanchor = "middle",
                            showarrow = FALSE,
                            font = list(size = 20,
                                        color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         # legend = list(orientation = "h",  
         #               xanchor = "center",
         #               yanchor = "bottom",
         #               x = 0.5,
         #               y = -0.125,
         #               font = list(color = "white")),
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=65),
         showlegend=F) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )%>%
  partial_bundle() 
```


### AA
```{r}
fig <- subplot(CA_1_1,CA_2_1, nrows = 2, shareX=T,titleX=F,margin=0.04) %>%
  partial_bundle() 
fig <- fig %>% layout(xaxis2 = list(domain=list(x=c(0,1),y=c(0,0.5))),
                      xaxis = list(domain=list(x=c(0,1),y=c(0.5,1))),
                      legend = list(orientation = "h",  
                                    xanchor = "center",
                                    yanchor = "bottom",
                                    x = 0.5,
                                    y = -0.125,
                                    font = list(color = "white")),
                      annotations = list(
                        list(text = "Fecha de reporte",
                             x = 0.5,
                             y = -0.09,
                             yref = "paper",
                             xref = "paper",
                             showarrow = FALSE,
                             font = list(size = 16,
                                         color = "white")),
                        list(text = "Casos nuevos por día",
                             x = -0.1225,
                             y = 0.1,
                             yref = "paper",
                             xref = "paper",
                             showarrow = FALSE,
                             font = list(size = 16,
                                         color ="#98cbe1"),
                             textangle = -90),
                        list(text = "Casos acumulados (lineal)",
                             x = 1.1225,
                             y = 0.8,
                             yref = "paper",
                             xref = "paper",
                             showarrow = FALSE,
                             font = list(size = 16,
                                         color ="#ffd29f"),
                             textangle = -90)),
                      margin = list(l=60, r=60, b=20, t=50))%>%
  partial_bundle() 

fig
```


### BB
```{r}
fig <- subplot(CA_1_2,CA_2_2, nrows = 2, shareX=T,titleX=F,margin=0.04) %>%
  partial_bundle() 
fig <- fig %>% layout(xaxis2 = list(domain=list(x=c(0,1),y=c(0,0.5))),
                      xaxis = list(domain=list(x=c(0,1),y=c(0.5,1))),
                      legend = list(orientation = "h",
                                    font = list(color = "white",
                                                size=10),
                                    x = 0.5,
                                    y = -0.09,
                                    yref = "paper",
                                    xref = "paper",
                                    xanchor="center",
                                    yanchor="middle"),
                      annotations = list(
                        list(text = "Fecha de reporte",
                             x = 0.5,
                             y = -0.09,
                             yref = "paper",
                             xref = "paper",
                             showarrow = FALSE,
                             font = list(size = 16,
                                         color = "white")),
                        list(text = "Casos acumulados (Logarítmico)",
                             x = -0.1225,
                             y = 0.1,
                             yref = "paper",
                             xref = "paper",
                             showarrow = FALSE,
                             font = list(size = 16,
                                         color ="White"),
                             textangle = -90)
                        # list(text = "Casos acumulados (lineal)",
                        #      x = 1.1225,
                        #      y = 0.8,
                        #      yref = "paper",
                        #      xref = "paper",
                        #      showarrow = FALSE,
                        #      font = list(size = 16,
                        #                  color ="#ffd29f"),
                        #      textangle = -90)),
                      ),
                      margin = list(l=60, r=60, b=20, t=50))%>%
  partial_bundle() 

fig
```






Regional {.tabset data-width=500} 
-------------------------------------

### Acumulados - Lineal

```{r, message=F, warning=F}

plots <- lapply(vars.pos, function(var) {
  
  plot_ly(dep.pos_dep.pos.imp.new)%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(dep.pos.imp.new$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.pos,TRUE,FALSE),
              yaxis="y"
    )  %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(dep.pos$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.pos,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.pos,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4),
              yaxis="y2"
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(dep.pos[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.pos,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(dep.pos.imp.new$dat),
                                  max(dep.pos.imp.new$dat)),
                        color = "white",
                        tickformat= "%d-%b"),
           yaxis = list(side = 'left', title = 'Casos Nuevos por día', 
                        showgrid = T, gridcolor = "#818181", zeroline = F,
                        color = "#98cbe1",
                        range=list(0, roundUpNice(max(dep.pos_dep.pos.imp.new[paste0(var,"_2")],na.rm = T))),
                        autotick=F,
                        tick0=0,
                        dtick=roundUpNice(max(dep.pos_dep.pos.imp.new[paste0(var,"_2")],na.rm = T))/5),
           yaxis2 = list(side = 'right', overlaying = paste0("y",ifelse(which(vars.pos==var)==1,
                                                                        "",
                                                                        2*which(vars.pos==var)-1)),
                         title = '', 
                         showgrid = F, zeroline = F,
                         color = "#ffd29f",
                         range=list(0, roundUpNice(max(dep.pos_dep.pos.imp.new[var],na.rm = T))),
                         autotick=F,
                         tick0=0,
                         dtick=roundUpNice(max(dep.pos_dep.pos.imp.new[var],na.rm = T))/5),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.2,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 14,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)%>%
    partial_bundle() 
})

subplot(plots,nrows=5, shareX = T,titleX=F,
        margin = 0.0375) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Lineal",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Casos nuevos por día",
                x = -0.05,
                y = 0.7,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="#98cbe1"),
                textangle = -90),
           list(text = "Casos acumulados (lineal)",
                x = 1.05,
                y = 0.7,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="#ffd29f"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=50, r=50, b=75, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )%>%
  partial_bundle() 




```

### Acumulados - Lineal V.2

```{r, message=F, warning=F}

plots <- lapply(vars.pos, function(var) {
  
  dup.dep.wide %>% select(days.start,
                          paste0(var),
                          paste0(var,"_2"),
                          paste0(var,"_3"),
                          paste0(var,"_4"),
                          paste0(var,"_5")) %>%
    group_by(days.start) %>% summarize_all(list(max),na.rm=T) %>%
    plot_ly() %>%
    add_lines(x = ~days.start, 
              y = as.formula(paste0("~", var)),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
'),
              name = ifelse(var == last.pos,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.pos,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4),
              yaxis="y"
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(dep.pos[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.pos,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )  %>%
    add_trace(x = ~days.start, y = as.formula(paste0("~", var,"_2")), 
              type = 'scatter',
              mode = 'lines', 
              name = 'Un (1) día',
              line = list(color = '#0e5871',
                          dash = "dash",
                          width=3.5),
              text = "Casos se duplican en un (1) día",
              hoverinfo = "text",
              showlegend=F) %>% 
    add_trace(x = ~days.start, y = as.formula(paste0("~", var,"_3")), 
              type = 'scatter',
              mode = 'lines', 
              name = 'Dos (2) días',
              line = list(color = '#006b7d',
                          dash = "dash",
                          width=3.5),
              text = "Casos se duplican en dos (2) días",
              hoverinfo = "text",
              showlegend=F) %>% 
    add_trace(x = ~days.start, y = as.formula(paste0("~", var,"_4")), 
              type = 'scatter',
              mode = 'lines', 
              name = 'Tres (3) días',
              line = list(color = '#007e7b',
                          dash = "dash",
                          width=3.5),
              text = "Casos se duplican en tres (3) días",
              hoverinfo = "text",
              showlegend=F) %>% 
    add_trace(x = ~days.start, y = as.formula(paste0("~", var,"_5")), 
              type = 'scatter',
              mode = 'lines', 
              name = 'Cuatro (4) días',
              line = list(color = '#008f6a',
                          dash = "dash",
                          width=3.5),
              text = "Casos se duplican en cuatro (4) días",
              hoverinfo = "text",
              showlegend=F)  %>%
    layout(xaxis = list(range = c(min(dup.dep.wide$days.start),
                                  max(dup.dep.wide$days.start)),
                        color = "white"),
           yaxis = list(side = 'left', 
                        title = list(text= 'Total de casos acumulados', 
                                     font = list(size = 16,
                                                 color = "White"),
                                     standoff = 15),   
                        type="log", automargin = T,
                        range = c(min(0),max(6)), 
                        showgrid = T, gridcolor = "#818181", zeroline = FALSE,
                        tickmode = "linear",
                        tick0 = 0,
                        color ="White"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.2,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 14,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)%>%
    partial_bundle() 
})

subplot(plots,nrows=5, shareX = T,titleX=F,
        margin = 0.0375) %>%
  layout(title = list(text = "Total de casos confirmados - Regiones",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Días desde el primer reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Casos acumulados (Logarítmica)",
                x = -0.05,
                y = 0.7,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="White"),
                textangle = -90)),
         # list(text = "Casos acumulados (lineal)",
         #      x = 1.05,
         #      y = 0.7,
         #      yref = "paper",
         #      xref = "paper",
         #      showarrow = FALSE,
         #      font = list(size = 16,
         #                  color ="#ffd29f"),
         #      textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=50, r=50, b=75, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )%>%
  partial_bundle() 

```


### Acumulados - Logaritmico

```{r, message=F, warning=F}

plots <- lapply(vars.pos, function(var) {
  
  plot_ly(dep.pos) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(dep.pos$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.pos,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.pos,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(dep.pos[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.pos,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(dep.pos$dat),
                                  max(dep.pos$dat)),
                        color = "white"),
           yaxis = list(color = "white", type = "log", tickmode = "linear"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Logarítmico",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Total de casos confirmados",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  plotly_config



```


Casos Nuevos {.bg}
=====================================  

Mapas {.tabset data-width=250} 
-------------------------------------
### Casos nuevos

```{r, message=F, warning=F}
x <- c.dep %>% dplyr::mutate(pos.new = ifelse(pos.new==0,NA, pos.new)) %>% .$pos.new


labels.new <- sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos.new) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette="RdPu", 
                           domain = log(x), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles() %>%
  map_poly (y=x,
            z=labels.new) %>%
  addLegend("bottomleft", pal=pal.cases, values = log(x), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  map_bounds()

rm(x)
```


Column 2 {.tabset data-width=300} 
-------------------------------------

### Diario y media móvil - Lineal

```{r, message=F, warning=F}
plot_ly(nac) %>%
  add_trace(x = ~dat, y = ~pos.new,
            type = 'scatter',
            mode = 'lines', name = 'Casos Nuevos por día',
            line = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~dat, y = ~mav.pos.new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil de casos por día',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac$pos.new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = ' Casos nuevos por día y media móvil',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos nuevos (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac$pos.new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Media Móvil - logarítmica

```{r, message=F, warning=F}
plot_ly(nac) %>%
  add_trace(x = ~dat, y = ~mav.pos.new,
            type = 'scatter', mode="lines",name = 'Casos Nuevos',
            line = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~dat, y = ~mav.pos.new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac$mav.pos.new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Media móvil (7d) y casos nuevos por día - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white", type ="log",tickmode="linear"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Media móvil de casos nuevos - 7 días (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac$mav.pos.new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Duplicación de la media móvil

```{r, message=F, warning=F}
plot_ly(dup.nac)%>% 
  add_trace(x = ~dat, y = ~dup.1,
            mode = 'lines', 
            name = 'Un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.2,
            mode = 'lines', 
            name = 'Dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.3,
            mode = 'lines', 
            name = 'Tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.4,
            mode = 'lines', 
            name = 'Cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en cuatro (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')%>%
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1')   %>% 
  layout(title = list(text= 'Tiempo de duplicación de casos acumulados',
                      font = list(
                        size = 20,
                        color="white")),
         xaxis = list(title = list(text="Días desde el primer reporte",
                                   standoff = 15),
                      range = c(as.Date(min(f.date)),max(today+15)),
                      color ="white",
                      tickformat= "%d-%b"),
         yaxis = list(side = 'left', 
                      title = list(text= 'Total de casos acumulados', 
                                   font = list(size = 16,
                                               color = "white"),
                                   standoff = 15),   
                      type="log", automargin = T,
                      range = c(min(0),max(6)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(title=list(text="Casos se duplican en...",
                                  font = list(color="white"),
                                  side="top"),
                       orientation = "h",
                       yref = "paper",
                       xref = "paper",
                       xanchor = "right",
                       yanchor = "bottom",  
                       x = 1,
                       y = 0.1,
                       font = list(color = "white"), 
                       automargin = T),
         annotations = list(xref='paper',
                            yref='paper',
                            x=0,
                            y=-0.1,
                            xanchor='left',
                            yanchor='bottom',
                            text='',
                            showarrow=FALSE,
                            font = list(size = 16,
                                        color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=0, r=0, b=20, t=65)
  ) %>%
  plotly_config( )

```


```{r}
dup.nac%>%
  dplyr::filter(days.end<=7 )%>%
  dplyr::mutate(days.start = as.numeric(difftime(dat,first(dat), units="days")),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                dup.6 = exp((log(2)/6)*days.start),
                dup.8 = exp((log(2)/8)*days.start),
                pos.sim = exp(((max(.$days.start)-min(.$days.start))/min(.$days.start))*(days.start))) %>%
  plot_ly()%>%
  add_trace(x = ~dat, y = ~pos.sim, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dat, y = ~dup.1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.8,
            mode = 'lines', 
            name = 'Casos se duplican en ocho (8) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en ocho (8) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = '',
         titlefont=list(color="white"),
         xaxis = list(title = "Últimos 7 días",
                      range = c(as.Date(min(f.date)),max(today+15)),
                      color ="white"),
         yaxis = list(side = 'left', title = '', type="log",
                      range = c(min(0),max(3)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )



```




















Column 3 {.tabset data-width=350} 
-------------------------------------
```{r, message=F, warning=F}
y<- dep.pos.imp.new 
colnames(y) <- paste(colnames(y), "2", sep = "_")

y<- y %>% 
  select(-c("dat_2","days.end_2")) %>% 
  cbind(dep.mav.pos.new)

```

### Lineal
```{r, message=F, warning=F}

plots <- lapply(vars.mav.new, function(var) {
  
  plot_ly(y) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.mav.new,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(y$dat),
                                  max(y$dat)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  plotly_config()

```

### Logaritmica 
```{r, message=F, warning=F}

plots <- lapply(vars.mav.new, function(var) {
  
  plot_ly(y) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.mav.new,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(y$dat),
                                  max(y$dat)),
                        color = "white"),
           yaxis = list(color = "white", type="log"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```


Fallecidos {.bg}
===================================== 

Column 1 {.tabset data-width=250} 
-------------------------------------



Column 1 {.tabset data-width=300} 
-------------------------------------



Column 1 {.tabset data-width=350} 
-------------------------------------

Fallecidos Nuevos {.bg}
===================================== 


Diagnósticos {.bg}
===================================== 



Diagnósticos Nuevos {.bg}
=====================================